Viruses. From Understanding to Investigation

Description

Front Cover Viruses Copyright Page Contents About the Author Preface Acknowledgments 1 Introduction to Animal Viruses What Is a Virus? Diversity in the World of Viruses Are Viruses Alive? Basic Steps in the Virus Replication-Cycle Growing Viruses Categorizing Viruses (Taxonomy) Outcomes of Viral Infection Introduction to Viral Pathogenesis Introduction to Virus Transmission 2 Virus Structure Anatomy of a Virus Capsid Structure and Function Capsids Are Built From Many Copies of One or a Few Types of Protein Simple Icosahedral Capsids Larger Icosahedral Capsids Polyomavirus and Papillomavirus Capsids Adenovirus Capsids Reoviruses Herpesvirus Capsids Poxvirus Structure Viral Envelopes Glycosylation Other Membrane Proteins Matrix Proteins Nucleocapsid Structure 3 Virus Interactions With the Cell Virus Interactions with the Cell The Extracellular Space The Plasma Membrane Attachment Occurs at the Plasma Membrane Virus Penetration and Uncoating at the Plasma Membrane Virus Penetration and Uncoating From Membrane Bound Vesicles Membrane Fusion Uncoating the Genome Cytoskeleton Movement Through the Cell, Interactions With the Cytoskeleton Virus Assembly Virion Release Virion Maturation Amplification of Viral Proteins and Nucleic Acids in the Context of the Infected Cell A Short Review of Transcription in the Eukaryotic Host Cell Transcription of Viral mRNAs A Short Review of Translation in the Eukaryotic Host Cell Translation of Viral Proteins Synthesis of Viral Genomes 4 Methods to Study Viruses Growing Viruses Generating Cell Cultures Purifying Viruses Visualizing Viruses Optical Microscopy Light Microscopes Fluorescence Microscopy Electron Microscopy Counting Viruses Infectivity Assays Chemical/Physical Methods of Virus Quantitation Hemagglutination Assay Serologic Techniques Hemagglutination Inhibition Assay Virus Neutralization Assay Enzyme-Linked Immunosorbent Assays Cell-Based Fluorescent Antibody Assays Western Blots Immunohistochemistry Detecting Viral Nucleic Acids Polymerase Chain Reaction High Throughput Sequencing Basic Principles of Diagnostic Virology References 5 Virus Transmission and Epidemiology Methods to Count Viral Infections and Disease Infection Versus Disease Developing Models of Virus Transmission Incubation, Latent, and Infectious Periods Virus Transmission 6 Immunity and Resistance to Viruses Innate Immunity Toll-Like Receptors Retinoic Acid-Inducible Gene-Like Receptors NLRs Are Receptors With NOD-Like Domains Inflammasomes Proinflammatory Molecules Interferons Type I IFNs Type II IFN Type III IFNs IFNs Bind to Receptors and Signal Through Janus Kinase Signal Transducers and Activators of Transcription Pathways IFN-Stimulated Genes and the Antiviral State Protein Kinase RNA-Activated Pathway 2′-5′ Oligo A Synthase Pathway Other Interferon Stimulated Genes Intrinsic Immunity Restriction Factors Autophagy Natural Killer Cell Responses to Viral Infection Specific Immunity Antibody Responses Cell-Mediated Responses Antigen Presentation Viruses Fight Back Antigenic Variation Suppression of Antigen Presentation Suppression of IFN Responses Suppression or Coopting of Apoptosis and Autophagy Immunosuppression Poxviruses Encode Molecules That Mimic Cytokines, IFNs, and Their Receptors Hiding From the Immune System 7 Viral Vaccines Classical versus Engineered Vaccines Vaccines Provide a Source of Antigens Replicating versus Inactivated Vaccines Killed, Inactivated, and Subunit Vaccines Viral Vaccines that contain Infectious Agents Antigen Recognition Correlates of Protection Vaccine Development A Final Word about Safety 8 Virus Evolution and Genetics Virus Evolution Virus Genetics Recombination Genotypes and Phenotypes Nonessential Genes Forward and Reverse Genetics Reverse Genetics of Positive-Strand RNA Viruses Reverse Genetics of Negative-Strand RNA Viruses Reverse Genetics of Retroviruses Reverse Genetics of DNA Viruses 9 Viral Pathogenesis Natural Barriers to Infection Primary Replication Movement to Secondary Replication Sites Genesis of Disease Immunopathogenesis Virulence Approaches to Study Viral Pathogenesis 10 Introduction to RNA Viruses Definition and Basic Properties of RNA Viruses Subgroups of RNA Viruses Positive Strand RNA Viruses Negative Sense and Ambisense RNA Viruses dsRNA Viruses Structural Features of RNA Virus Genomes Priming Viral RNA Synthesis Mechanisms to Generate Capped mRNAs Mechanisms to Generate Polyadenylated mRNAs Mechanisms to Regulate Synthesis of Genomes and Transcripts RNA Viruses and Quasispecies References 11 Family Picornaviridae Genome Organization Virion Structure Picornavirus Replication (Poliovirus Model) Binding and Penetration Translation Genome Replication Assembly Maturation Picornaviruses and Disease Genus Enterovirus Genus Hepatovirus Genus Apthovirus: Foot and Mouth Disease Virus 12 Family Caliciviridae Genome Organization Virion Structure General Replication Cycle Attachment/Penetration Genome Replication Translation Assembly/Release Diseases Acute Gasterointestinal Disease Feline Calicivirus Rabbit Calicivirus 13 Family Hepeviridae Genome Organization Virion Morphology General Replication Cycle of HEV Disease 14 Family Astroviridae Genome Organization Virion Morphology Diseases Caused by Astroviruses References 15 Family Flaviviridae Genome Structure/Organization Virion Structure General Overview of Replication Protein Products Diseases Genus Hepacivirus: Hepatitis C Virus Genus Flavivirus Yellow Fever Virus Dengue Fever Virus West Nile Virus Zika Virus: An Emerging Threat Genus Pestivirus References 16 Family Togaviridae Genome Structure Virion Structure Togavirus Replication Attachment and Penetration Translation Genome Replication Assembly and Release Transmission Alphaviruses Associated With Rash and Arthritis Chikungunya Virus Sindbis Virus Alphaviruses of Veterinary Importance Rubella Virus References 17 Family Coronaviridae Coronavirus Genome Organization Virion Structure Coronavirus Structural Proteins Coronavirus Replication Cycle Attachment Penetration Amplification RNA Synthesis Assembly and Release Diseases Caused by Coronaviruses Severe Acute Respiratory Syndrome Middle East Respiratory Syndrome Feline Coronavirus and Feline Infectious Peritonitis References 18 Family Arteriviridae Genome Organization Virion Structure Replication Cycle Diseases Caused by Arteriviruses Equine Viral Arteritis Porcine Reproductive and Respiratory Syndrome Simian Hemorrhagic Fever Virus and Related Viruses References 19 Family Rhabdoviridae Genome Organization Virus Structure Overview of Replication Attachment and Penetration Amplification The Switch from mRNA Synthesis to Genome Replication Assembly/Release Diseases Rabies and Rabies-Related Viruses Vesicular Stomatitis Virus Chandipura Virus Other Rhabdoviruses associated with Disease 20 Families Paramyxoviridae and Pneumoviridae Genome Structure/Organization Virion Structure Overview of Replication Attachment and Penetration Transcription Protein Synthesis Genome Replication Assembly, Release, and Maturation Diseases Measles Mumps Respiratory Tract Diseases Canine Distemper Henipaviruses Pneumoviruses 21 Family Filoviridae Genome Organization Virion Structure Overview of Replication Attachment/Penetration Transcription Translation Genome Replication Assembly Disease Entry Into Host Pathogenesis EBOV and MARV Antagonize Innate Immune Responses 22 Family Bornaviridae Genome Organization Virion Structure Overview of Replication Attachment and Penetration Transcription Protein Synthesis Genome Replication Assembly, Release, and Maturation Diseases Borna Disease Birds and Bornaviruses 23 Family Orthomyxoviridae Genome Structure/Organization Virion Structure Classification and Nomenclature of Orthomyxoviruses Overview of Replication Hemagglutinin Neuraminidase Matrix Protein (M1) M2 Nucleoprotein RNA Polymerase Complex Nuclear Export Protein Nonstructural Protein 1 Attachment/Penetration Transcription Translation Genome Replication Assembly, Budding, and Maturation Antigenic Drift and Antigenic Shift Disease Avian Influenza Antiviral Drugs Vaccines References 24 Family Bunyaviridae Genome Organization Virion Structure General Replication Strategy Attachment Penetration and Uncoating Amplification Assembly and Release Diseases La Crosse Virus Oropouche Virus Schmallenberg and Cache Valley Viruses Rift Valley Fever Virus Hantavirus Pulmonary Syndrome and Hantavirus Hemorrhagic Fever 25 Family Arenaviridae Genome Organization Virion Structure Overview of Replication Attachment/Penetration Transcription/Genome Replication Viral Proteins Assembly/Release Diseases Caused by Arenaviruses Lassa Fever Lymphocytic Choriomeningitis New World Arenaviruses 26 Family Reoviridae Genome Organization Virus Structure Overview of Replication Attachment/Entry Amplification Genome Replication Assembly, Maturation, and Release Diseases Genus Rotavirus Genus Orbivirus Genus Orthoreovirus Genus Coltivirus 27 Family Birnaviridae Genome Structure Virion Structure Replication Cycle Attachment/Penetration Amplification Assembly and Release Disease Infectious Bursal Disease (Gumboro) 28 Introduction to DNA Viruses Definition and Basic Properties of DNA Viruses Viral DNA Replication DNA Viruses and Cell Cycle Oncogenesis 29 Family Parvoviridae Genome Organization Virion Structure Overview of Replication Attachment/Penetration Genome Replication of Autonomous Parvoviruses Transcription and Translation Assembly Diseases Human B19 Parvovirus Feline Panleukopenia Virus Canine Parvovirus Aleutian Mink Disease 30 Other Small DNA Viruses Family Circoviridae Diseases Beak and Feather Disease Postweaning Multisystemic Wasting Syndrome Family Anelloviridae References 31 Family Polyomaviridae Genome Structure Virion Structure Replication Attachment and Penetration Early Transcription Genome Replication Late Transcription Assembly and Release Transformation Human Polyomaviruses and Disease 32 Family Papillomaviridae Genome Structure Virion Structure Replication Cycle Attachment/Penetration Early Transcription and Genome Replication Late Transcription and Vegetative DNA Replication Disease Human Papillomaviruses Other Cancers Caused by Human Papillomavirus Epidermodysplasia Verruciformis Animal Papillomaviruses 33 Family Adenoviridae Genome Organization Virion Structure Adenovirus Replication Cycle Attachment/Penetration Early Transcription E1A E1B E2 E3 Viral DNA Replication Late Transcription VA RNAs Assembly and Release Adenoviruses and Human Disease Adenoviruses and Transformation Oncolytic Adenoviruses Adenoviral Vectors 34 Family Herpesviridae Genome Organization Virus Structure Replication Cycle Attachment/Penetration Transcription/DNA Replication Assembly/Release Latency Diseases Caused by Human Herpesviruses HHV-1 and 2 Disease HHV-3 (Varicella Zoster Virus) HHV-4 (Epstein–Barr Virus) HHV-4 and Burkitt Lymphoma HHV-4 and Nasopharyngeal Carcinoma HHV-5 (Cytomegalovirus) HHV-6 and 7 HHV-8 (Kaposi Sarcoma Herpesvirus) Monkey B Herpesvirus Antiherpesviral Drugs References 35 Family Poxviridae Genome Organization Virion Structure Replication Attachment/Penetration Transcription and Genome Replication Assembly/Release Immune Avoidance Diseases Smallpox Molluscum Contagiosum Monkeypox Rabbit Myxoma Virus References 36 Family Retroviridae Virion Structure Genome Organization Overview of the Retroviral Replication Cycle The Process of Reverse Transcription Integration Transcription of Retroviral mRNA Structural Proteins Assembly, Release, and Maturation Mechanisms of Retroviral Oncogenesis 37 Replication and Pathogenesis of Human Immunodeficiency Virus History of HIV and Acquired Immunodeficiency Syndrome HIV is a Lentivirus HIV Proteins GAG Precursor (Pr55Gag) GAG-POL Polyprotein Precursor (Pr160Gag-pol) Protease Reverse Transcriptase Integrase ENV Precursor TAT REV Other HIV-1 Proteins Virus Infectivity Factor Viral Protein U Viral Protein R Viral Protein X is Unique to HIV-2 NEF Summary of HIV Replication Binding/Entry Reverse Transcription Nuclear Entry and Integration Transcription and Translation Assembly/Release/Maturation Overview of HIV Pathogenesis HIV-1 Infection of CD4+ T-Lymphocytes HIV-1 Infection of Monocytes and Macrophages HIV-1 Infection of Dendritic Cells Disruption of Immune Function Immune Activation HIV Transmission Disease Course Antiretroviral Drugs Entry/Fusion Inhibitors Nucleoside/Nucleoside Reverse Transcriptase Inhibitors Nonnucleoside Reverse Transcriptase Inhibitors Integrase Inhibitors Protease Inhibitors Combination Drugs Vaccines 38 Family Hepadnaviridae Genome Organization Virion Structure Replication Cycle Attachment/Penetration Transcription Genome Replication Assembly/Release of Infectious Particles Hepatitis B Virus and Disease Index Back Cover